Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2520
Accession number U67769
Name TW392
Submitted to NCBI 1996

U67769 isolate has foldings of [PBS region] [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [USE region] [227nt 3' terminus] [Complete poly(A) region] [USE, TAR, polyA] .

The region encompassing 227 nt 3' terminus

The primary sequence:

ctaaccctca gatgctgcat aaaagcagct gctttttgct tgtactgggt ctctctggtt agaccaggtc tgagcccggg agctctctgg ctagcaaggg aacccactgc ttaaagcctc aataaagctt gccttgagtg cttaaagtgg tgtgtgcccg tctgtgttag gactctggta actagagatc cctcagacca ctctagactg agta-aaaatc tctagca

The optimal secondary structure:

The suboptimal structures within ΔΔG ≤ 4 kcal/mole of the minimum free energy